Digital Commons Network^™

Integrating Clinical Cancer And Ptm Proteomics Data Identifies A Mechanism Of Ack1 Kinase Activation, Eranga R. Balasooriya, Deshan Madhusanka, Tania P. López-Palacios, Riley J. Eastmond, Dasun Jayatunge, Jake J. Owen, Jack S. Gashler, Christina M. Egbert, Chanaka Bulathsinghalage, Lu Liu, Stephen R. Piccolo, Joshua L. Andersen

Faculty Publications

Beyond the most common oncogenes activated by mutation (mut-drivers), there likely exists a variety of low-frequency mut-drivers, each of which is a possible frontier for targeted therapy. To identify new and understudied mut-drivers, we developed a machine learning (ML) model that integrates curated clinical cancer data and posttranslational modification (PTM) proteomics databases. We applied the approach to 62,746 patient cancers spanning 84 cancer types and predicted 3,964 oncogenic mutations across 1,148 genes, many of which disrupt PTMs of known and unknown function. The list of putative mut-drivers includes established drivers and others with poorly understood roles in cancer. This ML …

Editorial: An Unexpected Event Related To The Aquatic Mammals Of Latin America, Daniel Gonzalez-Socoloske

Faculty Publications

No abstract provided.

Energy, Passivity, And Morphological Capacities, Pablo Borja, Cosimo Della Santina, Azita Dabiri

School of Engineering, Computing and Mathematics

The morphology of a system may be exploited to reduce the controller workload or to perform specific tasks, e.g., locomotion processes. However, understanding and characterizing these capacities in terms of physical quantities remains an open problem. In this paper, we pose the question: are energy and dissipation useful physical quantities to characterize morphological capacities? First, to illustrate the relevance of this question, we present some basic concepts of passivity theory that are useful for carrying out an energy-based analysis of the behavior of dynamical systems. Then, we analyze the behavior of a mechanical system, and we show how its morphology …

Derivation, Validation, And Clinical Relevance Of A Pediatric Sepsis Phenotype With Persistent Hypoxemia, Encephalopathy, And Shock, L. Nelson Sanchez-Pinto, Tellen D. Bennett, Emily K. Stroup, Yuan Luo, Mihir Atreya, Juliane Bubeck-Wardenburg, Grace Chong, Alon Geva, E. Vincent S. Faustino, Reid W. Farris, Mark W. Hall, Colin Rogerson, Sareen S. Shah, Scott L. Weiss, Robinder G. Khemani

2020-Current year OA Pubs

OBJECTIVES: Untangling the heterogeneity of sepsis in children and identifying clinically relevant phenotypes could lead to the development of targeted therapies. Our aim was to analyze the organ dysfunction trajectories of children with sepsis-associated multiple organ dysfunction syndrome (MODS) to identify reproducible and clinically relevant sepsis phenotypes and determine if they are associated with heterogeneity of treatment effect (HTE) to common therapies.

DESIGN: Multicenter observational cohort study.

SETTING: Thirteen PICUs in the United States.

PATIENTS: Patients admitted with suspected infections to the PICU between 2012 and 2018.

INTERVENTIONS: None.

MEASUREMENTS AND MAIN RESULTS: We used subgraph-augmented nonnegative matrix factorization to …

Allogeneic Hematopoietic Cell Transplantation Improves Outcome In Myelodysplastic Syndrome Across High-Risk Genetic Subgroups: Genetic Analysis Of The Blood And Marrow Transplant Clinical Trials Network 1102 Study, Jurjen Versluis, Peter Westervelt, Et Al.

2020-Current year OA Pubs

PURPOSE: Allogeneic hematopoietic cell transplantation (HCT) in patients with myelodysplastic syndrome (MDS) improves overall survival (OS). We evaluated the impact of MDS genetics on the benefit of HCT in a biological assignment (donor

METHODS: We performed targeted sequencing in 309 patients age 50-75 years with International Prognostic Scoring System (IPSS) intermediate-2 or high-risk MDS, enrolled in the Blood and Marrow Transplant Clinical Trials Network 1102 study and assessed the association of gene mutations with OS. Patients with

RESULTS: The distribution of gene mutations was similar in the donor and no donor arms, with

CONCLUSION: HCT improved OS compared with non-HCT …

Calculation Of Atp Production Rates Using The Seahorse Xf Analyzer, Brandon R. Desousa, Kristen K.O. Kim, Anthony E. Jones, Andréa B. Ball, Wei Y. Hsieh, Pamela Swain, Danielle H. Morrow, Alexandra J. Brownstein, David A. Ferrick, Orian S. Shirihai, Andrew Neilson, David A. Nathanson, George W. Rogers, Brian P. Dranka, Anne N. Murphy, Charles Affourtit, Steven J. Bensinger, Linsey Stiles, Natalia Romero, Ajit S. Divakaruni

School of Biomedical Sciences

Oxidative phosphorylation and glycolysis are the dominant ATP-generating pathways in mammalian metabolism. The balance between these two pathways is often shifted to execute cell-specific functions in response to stimuli that promote activation, proliferation, or differentiation. However, measurement of these metabolic switches has remained mostly qualitative, making it difficult to discriminate between healthy, physiological changes in energy transduction or compensatory responses due to metabolic dysfunction. We therefore present a broadly applicable method to calculate ATP production rates from oxidative phosphorylation and glycolysis using Seahorse XF Analyzer data and empirical conversion factors. We quantify the bioenergetic changes observed during macrophage polarization as …

Nightmares And Self-Injury Among High-Risk Adolescents: Examining The Role Of Emotion Regulation, Kinjal K. Patel

Psychology Theses & Dissertations

Self-injurious thoughts and behaviors (SITBs) are a public health concern among youth. SITB rates rise drastically during adolescence -- a critical and sensitive developmental period characterized by dramatic changes in biological and social systems. Prior research has identified distal risk factors which tell us who is at risk for SITBs. Emerging research suggests proximal risk factors may be useful to identify when an individual may be at risk for SITBs. One promising proximal risk factor for SITBs is sleep problems. Although the relation between sleep problems and SITBs has been widely documented, little is known about the short-term, proximal links …

Emotional Intelligence In Difficult Decision-Making: A Multiple-Case Study Of Community College Academic Deans, Ekaterina Kalinina Brooks

Educational Leadership & Workforce Development Theses & Dissertations

The decisions made by leaders noticeably impact employee morale and influence the fulfillment of the organizational mission. However, making decisions can be challenging when options are complex and involve multiple risks and benefits. Navigating such decisions in an era of technology when decisions are more transparent than ever before can be particularly difficult for academic deans in community colleges. These mid-level administrators often face internal conflicts stemming from the nature of their positions, campus politics, and the challenge of working between the competing interests of faculty and senior leaders.

Over the last three decades, research has pointed out that strong …

Combination Therapy Of Triple-Negative Breast Cancer With Paclitaxel And Ambrisentan, A Selective Antagonist Of The Endothelin Type A Receptor, Inhibits Tumor Growth And Metastasis, Farah Nasser Almahrook

Theses

Cancer treatment is a big challenge especially when associated with metastasis. Moreover, the importance of using combination therapy is increasing, especially for highly invasive, drug-resistant cancers, such as triple-negative breast cancer (TNBC). Ambrisentan, a selective antagonist of the endothelin type A receptor (ETAR) was previously shown to reduce metastasis of TNBC in a preclinical tumor model when used prophylactically. In the current study, we investigated the therapeutic potential of Ambrisentan, given as monotherapy or in combination with Paclitaxel, on TNBC. The data show that oral dosing with Ambrisentan led to a significant retardation in tumor growth and metastasis. Moreover, combining …

Identification Of A Potential Pr50gag Binding Site Critical For Selective Encapsidation Of Feline Immunodeficiency Virus (Fiv) Genomic Rna, Anjana Krishnan

Dissertations

Feline immunodeficiency virus (FIV) is an important lentivirus that causes acquired immunodeficiency syndrome (AIDS) in cats, making FIV a potential small animal model for studying the pathogenesis of human AIDS. Furthermore, due to its phylogenetic distance from primate retroviruses like human immunodeficiency virus (HIV) and its ability to infect non-dividing cells, FIV is also being exploited for the development of vectors for human gene therapy. Therefore, it is of paramount importance that pertinent steps in the life cycle of FIV, such as genomic RNA (gRNA) packaging, are delineated at the molecular level. The process of retroviral gRNA packaging relies on …

Attention-Based Human Age Estimation From Face Images To Enhance Public Security, Md. Ashiqur Rahman, Shuhena S. Aonty, Kaushik Deb, Iqbal H. Sarker

Research outputs 2022 to 2026

Age estimation from facial images has gained significant attention due to its practical applications such as public security. However, one of the major challenges faced in this field is the limited availability of comprehensive training data. Moreover, due to the gradual nature of aging, similar-aged faces tend to share similarities despite their race, gender, or location. Recent studies on age estimation utilize convolutional neural networks (CNN), treating every facial region equally and disregarding potentially informative patches that contain age-specific details. Therefore, an attention module can be used to focus extra attention on important patches in the image. In this study, …

Spontaneous Collapse As A Prognostic Marker For Human Blastocysts: A Systematic Review And Meta-Analysis, Kate Bickendorf, Fang Qi, Kelli Peirce, Jay Natalwala, Vincent Chapple, Yanhe Liu

Research outputs 2022 to 2026

STUDY QUESTION: Is spontaneous collapse (SC) by human blastocysts a prognostic factor in IVF treatment? SUMMARY ANSWER: SC in human blastocyst is associated with reduced euploid embryo and pregnancy rates. WHAT IS KNOWN ALREADY: SC of the human blastocyst is a phenomenon that was revealed relatively recently following the clinical application of time-lapse monitoring in IVF laboratories. The ploidy and clinical prognosis of affected blastocysts are still poorly understood, with inconsistent reports. Systematic reviews and meta-analyses on this topic are currently absent in the literature but its potential as a marker of embryo viability holds great clinical value. In this …

Physical-Vapor-Deposited Metal Oxide Thin Films For Ph Sensing Applications: Last Decade Of Research Progress, Mohammad Nur-E-Alam, Devendra K. Maurya, Boon K. Yap, Armin Rajabi, Camellia Doroody, Hassan B. Mohamed, Mayeen U. Khandaker, Mohammad A. Islam, Sieh K. Tiong

Research outputs 2022 to 2026

In the last several decades, metal oxide thin films have attracted significant attention for the development of various existing and emerging technological applications, including pH sensors. The mandate for consistent and precise pH sensing techniques has been increasing across various fields, including environmental monitoring, biotechnology, food and agricultural industries, and medical diagnostics. Metal oxide thin films grown using physical vapor deposition (PVD) with precise control over film thickness, composition, and morphology are beneficial for pH sensing applications such as enhancing pH sensitivity and stability, quicker response, repeatability, and compatibility with miniaturization. Various PVD techniques, including sputtering, evaporation, and ion beam …

Soil Adsorption Of Heavy Metals To Protect Groundwater Near Refinery Wastewater Discharge Points, Hamid A. Al-Falahi, Ferdous A. Jabir, Muthanna H. Al-Dahhan

Chemical and Biochemical Engineering Faculty Research & Creative Works

This study presents a strategy to manage the discharge of wastewater, which is either partially treated or untreated, to safeguard the groundwater reserves in the region. a case study involving Ad Diwaniyah refinery wastewater disposal into an adjacent desert was utilized to evaluate the influence of soil adsorption on the attenuation of Pb, Cu, and Cd ion concentrations. Investigation of competitive adsorption of heavy metal ions (Pb2+, Cu2+, and Cd2+) in Dolomite-Limestone soil was conducted through batch and column methods. the adsorption behavior of the bivalent metal cations was observed to be pH dependent. However, the competitive extraction of the …

Catching Elusive Depression Via Facial Micro-Expression Recognition, Xiaohui Chen, Tony Tie (T.) Luo

Computer Science Faculty Research & Creative Works

Depression is a common mental health disorder that can cause consequential symptoms with continuously depressed mood that leads to emotional distress. One category of depression is Concealed Depression, where patients intentionally or unintentionally hide their genuine emotions through exterior optimism, thereby complicating and delaying diagnosis and treatment and leading to unexpected suicides. In this article, we propose to diagnose concealed depression by using facial micro-expressions (FMEs) to detect and recognize underlying true emotions. However, the extremely low intensity and subtle nature of FMEs make their recognition a tough task. We propose a facial landmark-based Region-of-Interest (ROI) approach to address the …

A New View Of Chlorophyll Dynamics In The Southern Mid-Atlantic Bight From A Two-Year High-Resolution Spray Glider Survey, Francesco Lane

OES Theses and Dissertations

The southern Mid-Atlantic Bight (MAB) near Cape Hatteras, NC, USA, is likely a hotspot for the episodic export of carbon-rich shelf waters to the open ocean. Over a 2 year period, from March 2017 to May 2019, Spray gliders repeatedly occupied transects, along the slope and across the shelf, generating high-resolution chlorophyll fluorescence (fChl) data in the southern MAB. This study implements an fChl calibration method utilizing remotely sensing ocean color as a standard. We validate the method’s utility by demonstrating a reduction in post-calibration cross-mission fChl variability and demonstrating close correspondence between the calibrated fChl data and an in …

Relationship Between Learning Communities And Campus Residency On Sense Of Belonging Among First Year Undergraduates, Lanah Kathryn Stafford

Educational Leadership & Workforce Development Theses & Dissertations

In higher education, sense of belonging has been linked to improved outcomes such as retention and academic achievement (e,g., Pittman & Richmond, 2007). Previous research has also identified participation in learning communities and campus residency as interventions which improve sense of belonging for students in this context (e.g., Solanki et al., 2019; Soria & Roberts, 2021). However, little research has been conducted to empirically study sense of belonging as a multidimensional construct, and no research has investigated interactions between on-campus residency and learning community participation on its development.

Data were collected from 1,072 first-year students on the Sense of Belonging …

Exploring The Lived Experiences Of Self-Identified Politically Conservative Students In Graduate Counseling Programs In Public Universities, Elizabeth A. Orrison

Counseling & Human Services Theses & Dissertations

Professionals within the fields of social science predominantly identify as liberal (Woessner & Kelly-Woessner, 2015) and many issues related to politics, such as power and oppression, are inherent and central to the social science fields (Lerner, 2020). Past research has shown the potential for political bias in academia, which has been linked to the lack of representation of various political identities. Most research on political academic bias is not current, making it difficult to find relevant research on this topic published within the last ten years. Currently, there has been no identified research or scholarly production that specifically explores self-identified …

Cheiloscopy Examination And Classification Of Lip Prints With And Without Parafunctional Oral Habits: A Cross-Sectional Observation Study, Emily Smith Regan

Dental Hygiene Theses & Dissertations

Problem: Lip prints are unique and have potential for use as a human identifier. The purpose of this study was to observe possible cheiloscopy differences of individuals with and without parafunctional oral habits. Additionally, inter-rater reliability (IRR) of lip print examiners was observed. Methods: This IRB approved blinded cross-sectional observational study collected lip prints from sixty-six individuals using lipstick and adhesive tape to transfer lip prints to white bond paper for viewing purposes. Each set of included lip prints was divided into quadrants and dichotomized as those with or without an oral parafunctional habit. Each quadrant sample was manually analyzed …

Pulsed Electric Field Ablation: Mechanisms Of Differential Cell Sensitivity And Methods To Mitigate Neuromuscular Excitation, Emily Gudvangen

Biomedical Engineering Theses & Dissertations

Ablation therapies aim to destroy tumors while maintaining minimal damage to surrounding healthy tissue. Pulsed electric field (PEF) ablation targets the cell membrane during the destruction of tissues, which consequently spares extracellular structures such as ducts and blood vessels, leaving the framework for tissue regeneration. However, the utility of PEF is limited by neuromuscular excitation, causing pain and involuntary muscle contraction. To identify PEF protocols that efficiently ablate tissue while minimizing neuromuscular stimulation, various PEF protocols differing in pulse duration, shape, and repetition rate were tested. The ratio of cell death and nerve excitation thresholds, which determines the range of …

The Effects Of Self-Regulated Learning On Community College Students Metacognition, Motivation And Achievement In Geoscience Courses, Melani A. Loney

Educational Leadership & Workforce Development Theses & Dissertations

This study investigated the impact of training in self-regulated learning on community college, geoscience students’ achievement, metacognition, time management, and science motivation scales. The study also investigated the impact of SRL training on these outcomes as a function of gender and ethnicity. During the Fall of 2022, 70 community college geoscience students from 9 different classes participated in the study. The classes were bifurcated with one half of the students in each class randomly assigned to the SRL treatment and the other half to the control condition. Each week, for 10 weeks during the semester, students in the treatment group …

Dental Hygiene Students Reported Physiological Symptoms Associated With Wearing An N95 Respirator Mask, Peyton Shea Butler

Dental Hygiene Theses & Dissertations

Purpose: Physiological symptoms and comfort levels while wearing an N95 respiratory mask has not been examined with dental hygienists. The purpose of this study was to investigate dental hygiene students reported physiological symptoms and comfort perception while wearing an N95 respirator mask during patient care appointments. Methods: After IRB approval (IRB #1987754-2), a 16-item questionnaire was distributed through email to a convenience sample of 65 dental hygiene students. Questions assessed respiratory, dermatologic, cardiac, mask mouth and general physiological symptoms, as well as comfort levels. Additionally, participants were asked to respond to demographic questions and one open ended question inquiring about …

Organic Carbon Decay Mediated By Mesopelagic Microbial Communities, Noah Jonathan Craft

OES Theses and Dissertations

Substantial remineralization of organic carbon occurs in the mesopelagic zone (i.e., the biological pump), the efficiency of which is responsible for the oceans’ capacity to store carbon originally derived from the atmosphere. To better understand how a substrate’s composition influences its degradation by mesopelagic microbial communities, we added treatments made of live algal cells, dead particulate organic carbon and dissolved organic carbon from ¹⁴C-labeled algal cultures to mesopelagic water collected in-situ. Each incubation took place in the laboratory over a period of months, during which PO¹⁴C, DO¹⁴C, ATP, prokaryote abundances and biochemical fractions were measured. …

Machine Learning Approach To Activity Categorization In Young Adults Using Biomechanical Metrics, Nathan Q. C. Holland

Mechanical & Aerospace Engineering Theses & Dissertations

Inactive adults often have decreased musculoskeletal health and increased risk factors for chronic diseases. However, there is limited data linking biomechanical measurements of generally healthy young adults to their physical activity levels assessed through questionnaires. Commonly used data collection methods in biomechanics for assessing musculoskeletal health include but are not limited to muscle quality (measured as echo intensity when using ultrasound), isokinetic (i.e., dynamic) muscle strength, muscle activations, and functional movement assessments using motion capture systems. These assessments can be time consuming for both data collection and processing. Therefore, understanding if all biomechanical assessments are necessary to classify the activity …

Do Microplastics, Vibrio Bacteria, And Warming Water Temperatures Cause Disease In The Northern Star Coral, Astrangia Poculata?, Heather Leigh Sheffey

OES Theses and Dissertations

As marine plastic pollution increases, it becomes imperative to study the effects of microplastics on marine fauna. Marine plastic debris is a vector for disease to marine invertebrates (Lamb et al., 2018; Rotjan et al., 2019). In this context, studies have shown Astrangia poculata will consume microplastics as they do their normal food (Allen et al, 2017; Rotjan et al., 2019). Further, with temperatures increasing worldwide, there is a concern the virulence of disease-causing bacteria will increase (Vezzulli et al., 2015). In a series of manipulative laboratory experiments, this study quantified changes in respiration rates and visual health of Astrangia …

Biomechanical Adaptations While Performing Bilateral Drop Landings With A Unilateral Ankle Tape Application, Eric Daniel Jenkins

Rehabilitation Sciences Theses & Dissertations

Ankle sprains are the most common injury in sport and exercise performance, which makes the utilization of ankle taping a common procedure to both prevent potential sprain, as well as protect against reinjury. However, unilateral ankle taping may have unintended consequences on the mechanics of the ankle and other joints of both legs. The aim of this dissertation was to determine the effects of ankle taping on lower body kinetics and kinematics, stiffness, and coordination during a bilateral landing task.

Twelve female participants completed a total of 90 drop landings across two visits, randomized from landing platforms of 30, 45, …

Genotyping Of The Tick-Borne Pathogen Rickettsia Parkeri, Rebecca Lynn Ferrara

Biological Sciences Theses & Dissertations

Rickettsia parkeri is a pathogen of interest to public health as the causative agent of R. parkeri rickettsiosis. Amblyomma maculatum, a vector of R. parkeri, is currently undergoing a range expansion out of its historic range along the Gulf Coast of the United States, including northwards into Southeastern Virginia. Within this expansion front, the prevalence of R. parkeri within A. maculatum differs from the historic range; the historic range has a prevalence of 7.9- 38.6% while the expansion front in SE VA has a prevalence of 41.8-55.7%. While the reason for this disparity has not been established, one …

Third-Party Reactions To Performance Feedback, Daroon Mohammed Jalil

Psychology Theses & Dissertations

Although the provision of feedback has traditionally been treated as a dyadic event, I argue for the existence of a neglected third-party - the witness. Drawing from the dual process model of vicarious mistreatment and feedback intervention theory, I hypothesize that 1) third parties experience negative [positive] affect when witnessing an unjust [just] feedback event, 2) negative [positive] affect is stronger when feedback cues are self-referenced [task-referenced], and 3) negative [positive] affect is related to a subsequent decrease [increase] in feedback seeking intentions. Results from a 2x2 between-subjects experiment with 470 participants provide partial support for the hypotheses. Third-parties experienced …

Investigation Of Nanosecond Pulsed Electric Fields (Nspef) Induced Anti-Cancer Mechanism And Enhanced B16f10 Melanoma Cancer Treatment, Kamal Asadipour

Biomedical Engineering Theses & Dissertations

The use of nanosecond pulsed electric fields (nsPEF) has emerged as a promising area of research with vast implications across various scientific disciplines. The ability to generate ultra-short, high-voltage electric pulses has paved the way for numerous applications, ranging from fundamental investigations of biological phenomena to the development of innovative medical therapies. The aim of this thesis is to highlight the importance of nsPEF in two critical areas: 1) Understanding the impact of subtle postpulse waveforms through a comprehensive analysis of two common pulse generators and 2) using this knowledge to advance melanoma treatment by enhancing the therapeutic effect of …

Modified Vaccine Vectors To Understand Adjuvant Functions Of Listeria During Chronic Schistosomiasis, Stephanie K. Norwood

Biological Sciences Theses & Dissertations

Vaccination is one of the most effective strategies employed to prevent infectious diseases. Successful vaccination is dependent upon the induction of a specific, robust, and prolonged immune response. One of the major challenges faced by vaccine development is vaccine failure due to host-related factors that can modulate the immune system, which leads to non-responsiveness to vaccinations. The generation of new vaccine strategies is imperative to combat these effects. Live bacterial vectors are one approach used as they can elicit humoral immunity, cellular immunity, or both. Listeria monocytogenes is a Gram positive, intracellular pathogen that is an effective bacterial vaccine vector …